Bilash,
You need to prepare and load .prepi/.frcmod files for residues AMA and COLT
- at least - since they are not part of the force fields you have sourced.
The non-integral charge is another matter, as some slop is expected/common
but I'd rather see -1.0XXX than -1.194; this could be an artifact from not
having proper atom types/charges as mentioned above, or some other issue.
I suggest stepwise debugging: get the modifications for AMA and COLT
prepared/loaded/okayed and go from there.
Cheers,
Todd
On Fri, Dec 29, 2023 at 8:59 AM BILASH MAITY via AMBER <amber.ambermd.org>
wrote:
> Respected Amber community,
> I am trying to make a bond between Threonine and Mannose using Tleap.
> Here is my input file,
>
> source
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.GLYCAM_06j-1
> source
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/oldff/leaprc.ff14SB
> source
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.protein.ff14SB
> source /home/bilash/SOFTWARE/NEW_AMBER/amber18/dat/leap/cmd/leaprc.gaff
> list
> glyprot =loadpdb thr_man_tutorial.pdb
> bond glyprot.2.OG1 glyprot.1.C1
> savepdb glyprot man_thr_corr_amber.pdb
> saveamberparm glyprot man_thr-tutorial.top man_thr-tutorial.crd
> quit
>
> This is the error I am getting:
>
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
> Converting C-terminal residue name to PDB format: COLT -> OLT
> Checking Unit.
>
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
> There is a bond of 6.323369 angstroms between:
>
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
> The unperturbed charge of the unit (-1.194000) is not integral.
>
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Warning!
> The unperturbed charge of the unit (-1.194000) is not zero.
> FATAL: Atom .R<AMA 1>.A<C1 1> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H1 2> does not have a type.
> FATAL: Atom .R<AMA 1>.A<C5 3> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H5 4> does not have a type.
> FATAL: Atom .R<AMA 1>.A<O5 5> does not have a type.
> FATAL: Atom .R<AMA 1>.A<C2 6> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H2 7> does not have a type.
> FATAL: Atom .R<AMA 1>.A<O2 8> does not have a type.
> FATAL: Atom .R<AMA 1>.A<HO2 9> does not have a type.
> FATAL: Atom .R<AMA 1>.A<C3 10> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H3 11> does not have a type.
> FATAL: Atom .R<AMA 1>.A<O3 12> does not have a type.
> FATAL: Atom .R<AMA 1>.A<HO3 13> does not have a type.
> FATAL: Atom .R<AMA 1>.A<C4 14> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H4 15> does not have a type.
> FATAL: Atom .R<AMA 1>.A<O4 16> does not have a type.
> FATAL: Atom .R<AMA 1>.A<HO4 17> does not have a type.
> FATAL: Atom .R<AMA 1>.A<C6 18> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H61 19> does not have a type.
> FATAL: Atom .R<AMA 1>.A<H62 20> does not have a type.
> FATAL: Atom .R<AMA 1>.A<O6 21> does not have a type.
> FATAL: Atom .R<AMA 1>.A<HO6 22> does not have a type.
> FATAL: Atom .R<COLT 2>.A<HN 15> does not have a type.
> FATAL: Atom .R<COLT 2>.A<HG1 16> does not have a type.
> FATAL: Atom .R<COLT 2>.A<OT1 17> does not have a type.
> FATAL: Atom .R<COLT 2>.A<OT2 18> does not have a type.
>
> /home/bilash/SOFTWARE/NEW_AMBER/amber18/bin/teLeap: Fatal Error!
> Failed to generate parameters
>
> Exiting LEaP: Errors = 1; Warnings = 6; Notes = 1.
>
> If any one can suggest the solution that wil be very helpful.
>
> Thanking You,
> BILASH MAITY
>
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Received on Fri Dec 29 2023 - 08:00:03 PST
